publish-directory - Test repeat publish using --force mode

src/npg_irods/publish.py

@@ -67,7 +67,7 @@ def publish_directory(
             exists, the operation is skipped for that path. See DataObject.put() for
             more information. The default is False.
         force: If a data object is written, overwrite any data object already present
-            in iRODS. The default is True.
+            in iRODS. The default is False.
         handle_exceptions: Report a count of any errors encountered during publishing,
             rather than raising an exception. The default is True. If False and one or
             more errors are encountered, a PublishingError is raised from the first

tests/data/ultima/minimal/000001-a/000002-c.txt

@@ -0,0 +1 @@
+ee305ec7-dd05-43be-b266-f7bf5e21800c

tests/data/ultima/minimal/000001-a/000002-c.txt.md5

@@ -0,0 +1 @@
+ac06fd24fc0edc84761c799c975d73c3

tests/data/ultima/minimal/000001-d/000001-d.txt

@@ -0,0 +1 @@
+c18dee80-d2d4-44dc-8b8f-68161862fe12

tests/data/ultima/minimal/000001_a.txt

@@ -0,0 +1 @@
+615b338a-2e3f-4e41-861c-c8b03e11cf19

tests/data/ultima/minimal/000001_a.txt.md5

@@ -0,0 +1 @@
+6e785a5236e0b5480025469d312b2aeb

tests/data/ultima/minimal/b.txt

@@ -0,0 +1 @@
+0879abcc-5755-4620-9b43-f52f0c5f69ea

tests/data/ultima/minimal/b.txt.md5

@@ -0,0 +1 @@
+2b1c6c7095b550e86230c4996d1595e4

tests/helpers/__init__.py

@@ -19,10 +19,11 @@
 
 """Helper functions for testing."""
 
+import hashlib
 import os
 import subprocess
 from datetime import datetime
-from pathlib import PurePath
+from pathlib import PurePath, Path
 from os import PathLike
 
 import pytest
@@ -70,6 +71,7 @@
 ADMIN_AC = AC("irods", Permission.OWN, ZONE)
 PUBLIC_AC = AC("public", Permission.READ, ZONE)
 STUDY_AC = AC("ss_1000", Permission.READ, ZONE)
+STUDY2_AC = AC("ss_2000", Permission.READ, ZONE)
 UNMANAGED_AC = AC("unmanaged", Permission.READ, ZONE)
 """e.g. dnap-ro"""
 
@@ -241,3 +243,7 @@ def _run(cmd: list[str]):
         return
 
     raise RodsError(completed.stderr.decode("utf-8").strip())
+
+
+def get_md5(path: Path):
+    return hashlib.md5(path.read_bytes()).hexdigest()

tests/test_publish_directory.py

@@ -15,10 +15,19 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 import json
-from pathlib import Path, PurePath
+import shutil
+from pathlib import PurePath
 from unittest.mock import MagicMock, patch
 
-from helpers import is_inheritance_enabled, ADMIN_AC, PUBLIC_AC, STUDY_AC, UNMANAGED_AC
+from helpers import (
+    is_inheritance_enabled,
+    ADMIN_AC,
+    PUBLIC_AC,
+    UNMANAGED_AC,
+    STUDY2_AC,
+    history_in_meta,
+    get_md5,
+)
 from npg_irods.cli import publish_directory
 from pytest import LogCaptureFixture, MonkeyPatch
 from pytest import mark as m
@@ -71,7 +80,8 @@ def test_npg_publish_tree_compatibility_ultima(
         monkeypatch: MonkeyPatch,
     ):
         # Arrange
-        src = Path("./tests/data/ultima/minimal").absolute()
+        src = tmp_path / "minimal"
+        shutil.copytree("./tests/data/ultima/minimal", src)
         # empty_collection stands in for $ZONE/ultimagen/runs
         # SOP: Destination collection doesn't exist
         dest = (
@@ -85,39 +95,98 @@ def test_npg_publish_tree_compatibility_ultima(
         # Public
         root_metadata = tmp_path / "root_metadata.json"
         root_metadata.write_text(json.dumps([{"attribute": "a1", "value": "v1"}]))
-        self._main(
-            [
-                str(src),
-                str(dest),
-                "--group",
-                "public",
-                "--exclude",
-                f"{src}/000001-",
-                "--exclude",
-                ".md5",
-                "--metadata-file",
-                str(root_metadata),
-            ]
-        )
+        root_args = [
+            str(src),
+            str(dest),
+            "--force",
+            "--group",
+            "public",
+            "--exclude",
+            f"{src}/000001-",
+            "--exclude",
+            ".md5",
+            "--metadata-file",
+            str(root_metadata),
+        ]
+        self._main(root_args)
 
         # Study
         sample_metadata = tmp_path / "sample_metadata.json"
-        sample_metadata.write_text(json.dumps([{"attribute": "a2", "value": "v2"}]))
-        self._main(
-            [
-                str(src / "000001-a"),
-                str(dest / "000001-a"),
-                "--group",
-                "ss_1000#testZone",
-                "--exclude",
-                ".md5",
-                "--metadata-file",
-                str(sample_metadata),
-            ]
+        sample_metadata.write_text(
+            json.dumps(
+                [{"attribute": "a2", "value": "v2"}, {"attribute": "a3", "value": "v3"}]
+            )
         )
+        sample_dir_args = [
+            str(src / "000001-a"),
+            str(dest / "000001-a"),
+            "--force",
+            "--group",
+            "ss_1000#testZone",
+            "--exclude",
+            ".md5",
+            "--metadata-file",
+            str(sample_metadata),
+        ]
+        self._main(sample_dir_args)
 
         # Private
-        self._main([str(src / "000001-d"), str(dest / "000001-d")])
+        private_dir_args = [str(src / "000001-d"), str(dest / "000001-d"), "--force"]
+        self._main(private_dir_args)
+
+        # Repeated publish: No changes
+        self._main(root_args)
+        self._main(sample_dir_args)
+        self._main(private_dir_args)
+
+        # Repeated publish: New file
+        (src / "c.txt").write_text("new")
+        c_txt_original_md5 = get_md5(src / "c.txt")
+        self._main(root_args)
+        created_values = [
+            x
+            for x in DataObject(dest / "c.txt").metadata()
+            if x.attribute == "dcterms:created"
+        ]
+        assert len(created_values) == 1
+        c_txt_original_dcterms_created = created_values[0]
+
+        # Repeated publish: Modified file
+        (src / "c.txt").write_text("modified")
+        c_txt_modified_md5 = get_md5(src / "c.txt")
+        self._main(root_args)
+        created_values = [
+            x
+            for x in DataObject(dest / "c.txt").metadata()
+            if x.attribute == "dcterms:created"
+        ]
+        assert len(created_values) == 1
+        c_txt_modified_dcterms_created = created_values[0]
+        assert (
+            c_txt_modified_dcterms_created == c_txt_original_dcterms_created
+        ), "Original file creation date should not change when we update contents of the file"
+
+        # Repeated publish: Different group, different metadata, no file changes
+        sample_metadata_updated = tmp_path / "sample_metadata_updated.json"
+        # a2: Deleted
+        # a3: Updated
+        # a4: Added
+        sample_metadata_updated.write_text(
+            json.dumps(
+                [
+                    {"attribute": "a3", "value": "v3_updated"},
+                    {"attribute": "a4", "value": "v4"},
+                ]
+            )
+        )
+        sample_dir_updated_args = sample_dir_args.copy()
+        sample_dir_updated_args[sample_dir_updated_args.index("ss_1000#testZone")] = (
+            "ss_2000#testZone"
+        )
+        sample_dir_updated_args[sample_dir_updated_args.index(str(sample_metadata))] = (
+            str(sample_metadata_updated)
+        )
+        self._main(sample_dir_updated_args)
 
         # Assert
         assert is_inheritance_enabled(
@@ -142,9 +211,38 @@ def test_npg_publish_tree_compatibility_ultima(
             Collection(dest / "000001-d"),
             DataObject(dest / "000001_a.txt"),
             DataObject(dest / "b.txt"),
+            DataObject(dest / "c.txt"),
             DataObject(dest / "000001-a" / "000002-c.txt"),
             DataObject(dest / "000001-d" / "000001-d.txt"),
         ]
+        assert [x.attribute for x in DataObject(dest / "b.txt").metadata()] == [
+            "dcterms:created",
+            "dcterms:creator",
+            "md5",
+            "type",
+        ]
+
+        assert [x.attribute for x in DataObject(dest / "c.txt").metadata()] == [
+            "dcterms:created",
+            "dcterms:creator",
+            "md5",
+            "md5",
+            "type",
+        ]
+        assert [
+            x.value
+            for x in DataObject(dest / "c.txt").metadata()
+            if x.attribute == "md5"
+        ] == [
+            c_txt_original_md5,
+            c_txt_modified_md5,
+        ], "New md5 attribute should be added, previous preserved to provide history"
+        assert (
+            DataObject(dest / "c.txt").read() == "modified"
+        ), "Contents of data object in iRODS should have updated"
+        assert (
+            DataObject(dest / "c.txt").checksum() == c_txt_modified_md5
+        ), "Checksum should have updated"
 
         assert DataObject(dest / "000001_a.txt").acl() == [
             ADMIN_AC,
@@ -156,15 +254,46 @@ def test_npg_publish_tree_compatibility_ultima(
             PUBLIC_AC,
             UNMANAGED_AC,
         ]
+        assert DataObject(dest / "c.txt").acl() == [
+            ADMIN_AC,
+            PUBLIC_AC,
+            UNMANAGED_AC,
+        ]
 
         assert is_inheritance_enabled(dest / "000001-a")
-        assert Collection(dest / "000001-a").acl() == [ADMIN_AC, STUDY_AC, UNMANAGED_AC]
-        assert Collection(dest / "000001-a").metadata() == [AVU("a2", "v2")]
+        assert Collection(dest / "000001-a").acl() == [
+            ADMIN_AC,
+            STUDY2_AC,
+            UNMANAGED_AC,
+        ]
+        assert [
+            x
+            for x in Collection(dest / "000001-a").metadata()
+            if x.attribute != "a3_history"
+        ] == [
+            AVU("a2", "v2"),  # Earlier metadata preserved
+            AVU("a3", "v3_updated"),
+            AVU("a4", "v4"),
+        ]
+        assert history_in_meta(
+            AVU.history(AVU("a3", "v3")), Collection(dest / "000001-a").metadata()
+        )
+        assert len(Collection(dest / "000001-a").metadata()) == 4
+
         assert DataObject(dest / "000001-a" / "000002-c.txt").acl() == [
             ADMIN_AC,
-            STUDY_AC,
+            STUDY2_AC,
             UNMANAGED_AC,
         ]
+        assert [
+            x.attribute
+            for x in DataObject(dest / "000001-a" / "000002-c.txt").metadata()
+        ] == [
+            "dcterms:created",
+            "dcterms:creator",
+            "md5",
+            "type",
+        ]
 
         assert is_inheritance_enabled(dest / "000001-d")
         assert Collection(dest / "000001-d").acl() == [